chr10-52780137-G-A

Position:

• chr10-52780137-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_945963.2(LOC105378306):​n.386+594G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,112 control chromosomes in the GnomAD database, including 1,851 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1851 hom., cov: 31)
• Consequence: LOC105378306 XR_945963.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917

Genes affected

LOC105378306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378306	XR_945963.2	n.386+594G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21948 AN: 151994 Hom.: 1857 Cov.: 31

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21934 AN: 152112 Hom.: 1851 Cov.: 31 AF XY: 0.144 AC XY: 10678 AN XY: 74346

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.166

Alfa AF: 0.169 Hom.: 901

Bravo AF: 0.133

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11003137; hg19: chr10-54539897;